Related papers: Virus Structure: From Crick and Watson to a New Co…
In many virus families, tens to thousands of proteins assemble spontaneously into a capsid (protein shell) while packaging the genomic nucleic acid. This review summarizes recent advances in computational modeling of these dynamical…
The packaging of genetic material within a protein shell, called the capsid, marks a pivotal step in the life cycle of numerous single-stranded RNA viruses. Understanding how hundreds, or even thousands, of proteins assemble around the…
The majority of viruses are organised according to the structural blueprints of the seminal Caspar-Klug theory. However, there are a number of notable exceptions to this geometric design principle. Prominent examples are the cancer-causing…
We investigate the modifications brought about by the linear connectivity among charges in the classical Thomson problem. Instead of packing with local hexagonal order intersperced with topological defects, we find charge distributions with…
Nanoparticles with "sticky patches" have long been proposed as building blocks for the self-assembly of complex structures. The synthetic realizability of such patchy particles, however, greatly lags behind predictions of patterns they…
In this work we study how a viral capsid can change conformation using techniques of Large Deviations Theory for stochastic differential equations. The viral capsid is a model of a complex system in which many units - the proteins forming…
A quantum scar - an enhancement of a quantum probability density in the vicinity of a classical periodic orbit - is a fundamental phenomenon connecting quantum and classical mechanics. Here we demonstrate that some of the eigenstates of the…
We perform numerical simulations of purely repulsive soft colloidal particles interacting via a generalized elastic potential and constrained to a two-dimensional plane and to the surface of a spherical shell. For the planar case, we…
Single-stranded RNA viruses co-assemble their capsid with the genome and variations in capsid structures can have significant functional relevance. In particular, viruses need to respond to a dehydrating environment to prevent genomic…
Quantum many-body scars, long-lived excited states of correlated quantum chaotic systems that evade thermalization, are of great fundamental and technological interest. We create novel scar states in a bosonic 1D quantum gas of dysprosium…
The method of Morse theory is used to analyze the distributions of unit charges interacting through a repulsive force and constrained to move on the surface of a sphere -- the Thomson problem. We find that, due to topological reasons, the…
We present a generalized Landau-Brazovskii theory for the solidification of chiral molecules on a spherical surface. With increasing sphere radius one encounters first intervals where robust achiral density modulations appear with…
In the frame of the Landau-Ginzburg formalism we propose a minimal phenomenological model for a morphological transformation in viral capsid shells. The transformation takes place during virus maturation process which renders virus…
The coat proteins of many viruses spontaneously form icosahedral capsids around nucleic acids or other polymers. Elucidating the role of the packaged polymer in capsid formation could promote biomedical efforts to block viral replication…
We develop the theory of quantum scars for quantum fields. By generalizing the formalisms of Heller and Bogomolny from few-body quantum mechanics to quantum fields, we find that unstable periodic classical solutions of the field equations…
A simple model is proposed aimed to investigate how the amount of dissociated ions influences the mechanical stability of viral capsids. After an osmotic and mechanical equilibrium is established with the outer solution, a non-adiabatic…
Understanding the interplay between ordered structures and substrate curvature is an interesting problem with versatile applications, including functionalization of charged supramolecular surfaces and modern microfluidic technologies. In…
Unstable periodic orbits are known to originate scars on some eigenfunctions of classically chaotic systems through recurrences causing that some part of an initial distribution of quantum probability in its vicinity returns periodically…
Viruses are known to tolerate wide ranges of pH and salt conditions and to withstand internal pressures as high as 100 atmospheres. In this paper we investigate the mechanical properties of viral capsids, calling explicit attention to the…
Chaos plays a crucial role in numerous natural phenomena, but its quantum nature has remained large elusive. One intriguing quantum-chaotic phenomenon is the scarring of a single-particle wavefunction, where the quantum probability density…